Merge branch 'ml4ai:main' into main

Dockerfile.skema-rs

@@ -1,4 +1,4 @@
-from rust:1.70
+from rust:1.72.1
 
 # =====================
 # ENV setup for app

pyproject.toml

@@ -16,7 +16,7 @@ dependencies=[
  "dill==0.3.7",
  "networkx==2.8.8",
  "PyYAML",
- "tree-sitter",
+ "tree-sitter==0.20.4",
  "neo4j==5.14.1",
  "requests",
  "beautifulsoup4", # used to remove comments etc from pMML before sending to MORAE

skema/gromet/__init__.py

@@ -1,3 +1,3 @@
-GROMET_VERSION = "0.1.8"
+GROMET_VERSION = "0.1.9"
 
 __all__ = ["GROMET_VERSION"]

skema/gromet/fn/__init__.py

@@ -4,9 +4,9 @@
 """
  Grounded Model Exchange (GroMEt) schema for Function Networks
 
- This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/swagger_client/models/`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
+ This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/skema.gromet.fn.`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
 
- OpenAPI spec version: 0.1.8
+ OpenAPI spec version: 0.1.10
  Contact: [email protected]
  Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -22,11 +22,12 @@
 from skema.gromet.fn.gromet_fn import GrometFN
 from skema.gromet.fn.gromet_fn_module import GrometFNModule
 from skema.gromet.fn.gromet_fn_module_collection import GrometFNModuleCollection
+from skema.gromet.fn.gromet_fn_module_dependency_reference import GrometFNModuleDependencyReference
 from skema.gromet.fn.gromet_object import GrometObject
 from skema.gromet.fn.gromet_port import GrometPort
 from skema.gromet.fn.gromet_wire import GrometWire
 from skema.gromet.fn.import_source_type import ImportSourceType
 from skema.gromet.fn.import_type import ImportType
 from skema.gromet.fn.literal_value import LiteralValue
-# from skema.gromet.fn.metadata import Metadata
+from skema.gromet.fn.metadata import Metadata
 from skema.gromet.fn.typed_value import TypedValue

skema/gromet/fn/function_type.py

@@ -3,9 +3,9 @@
 """
  Grounded Model Exchange (GroMEt) schema for Function Networks
 
- This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/swagger_client/models/`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
+ This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/skema.gromet.fn.`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
 
- OpenAPI spec version: 0.1.8
+ OpenAPI spec version: 0.1.10
  Contact: [email protected]
  Generated by: https://github.com/swagger-api/swagger-codegen.git
 """
@@ -29,6 +29,8 @@ class FunctionType(object):
  PREDICATE = "PREDICATE"
  MODULE = "MODULE"
  ABSTRACT = "ABSTRACT"
+ LABEL = "LABEL"
+ GOTO = "GOTO"
  LANGUAGE_PRIMITIVE = "LANGUAGE_PRIMITIVE"
  IMPORTED = "IMPORTED"
  IMPORTED_METHOD = "IMPORTED_METHOD"

skema/gromet/fn/gromet_box.py

@@ -3,9 +3,9 @@
 """
  Grounded Model Exchange (GroMEt) schema for Function Networks
 
- This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/swagger_client/models/`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
+ This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/skema.gromet.fn.`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
 
- OpenAPI spec version: 0.1.8
+ OpenAPI spec version: 0.1.10
  Contact: [email protected]
  Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

skema/gromet/fn/gromet_box_conditional.py

@@ -3,9 +3,9 @@
 """
  Grounded Model Exchange (GroMEt) schema for Function Networks
 
- This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/swagger_client/models/`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
+ This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/skema.gromet.fn.`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
 
- OpenAPI spec version: 0.1.8
+ OpenAPI spec version: 0.1.10
  Contact: [email protected]
  Generated by: https://github.com/swagger-api/swagger-codegen.git
 """

skema/gromet/fn/gromet_box_function.py

@@ -3,9 +3,9 @@
 """
  Grounded Model Exchange (GroMEt) schema for Function Networks
 
- This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/swagger_client/models/`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
+ This document defines the GroMEt Function Network data model. Note that Metadata is defined in separate spec. __Using Swagger to Generate Class Structure__ To automatically generate Python or Java models corresponding to this document, you can use [swagger-codegen](https://swagger.io/tools/swagger-codegen/). This can be used to generate the client code based off of this spec, and in the process this will generate the data model class structure. 1. Install via the method described for your operating system [here](https://github.com/swagger-api/swagger-codegen#Prerequisites). Make sure to install a version after 3.0 that will support openapi 3. 2. Run swagger-codegen with the options in the example below. The URL references where the yaml for this documentation is stored on github. Make sure to replace CURRENT_VERSION with the correct version. (The current version is `0.1.7`.) To generate Java classes rather, change the `-l python` to `-l java`. Change the value to the `-o` option to the desired output location. ``` swagger-codegen generate -l python -o ./client -i https://raw.githubusercontent.com/ml4ai/automates-v2/master/docs/source/gromet_FN_v{CURRENT_VERSION}.yaml ``` 3. Once it executes, the client code will be generated at your specified location. For python, the classes will be located in `$OUTPUT_PATH/skema.gromet.fn.`. For java, they will be located in `$OUTPUT_PATH/src/main/java/io/swagger/client/model/` If generating GroMEt schema data model classes in SKEMA (AutoMATES), then after generating the above, follow the instructions here: ``` <automates>/automates/model_assembly/gromet/model/README.md ``` # noqa: E501
 
- OpenAPI spec version: 0.1.8
+ OpenAPI spec version: 0.1.10
  Contact: [email protected]
  Generated by: https://github.com/swagger-api/swagger-codegen.git
 """